The HIV genome is highly plastic due to a high mutation rate and functional compensation. This high mutation rate is driven by at least two mechanisms: the low fidelity of the viral reverse transcriptase (RT) resulting in at least one mutation per replication cycle, and the dual effects of the anti-retroviral cellular factor APOBEC3G gene and viral infectivity factor Vif accessory gene. Genomes with every possible mutation and many double mutations are generated during every replication cycle, resulting in tremendous antigenic diversity. Accordingly, it has been argued that a candidate vaccine derived from an individual isolate may not elicit sufficient cross reactivity to protect against diverse circulating HIV viruses. Recent studies have suggested that consensus immunogens (Gao, F., et al. 2005. Antigenicity and immunogenicity of a synthetic human immunodeficiency virus type 1 group m consensus envelope glycoprotein. J Virol 79:1154-63.; Scriba, T. J., et al. 2005. Functionally-inactive and immunogenic Tat, Rev and Nef DNA vaccines derived from sub-Saharan subtype C human immunodeficiency virus type 1 consensus sequences. Vaccine 23:1158-69) or ancestral immunogens (Doria-Rose, N. A., et al. 2005. Human Immunodeficiency Virus Type 1 subtype B Ancestral Envelope Protein Is Functional and Elicits Neutralizing Antibodies in Rabbits Similar to Those Elicited by a Circulating Subtype B Envelope. J. Virol. 79:11214-11224; Gao, F., et al. 2004. Centralized immunogens as a vaccine strategy to overcome HIV-1 diversity. Expert Rev. Vaccines 3:S161-S168; Mullins, J. I., et al. 2004. Immunogen sequence: the fourth tier of AIDS vaccine design. Expert Rev. Vaccines 3:S151-S159; Nickle, D. C., et al. 2003. Consensus and ancestral state HIV vaccines. Science 299:1515-1517) may be useful in this regard. However, the initial studies of these approaches showed relatively modest cellular immune enhancement induced by these immunogens.
Recently Derdeyn et al. analyzed HIV-1 subtype C envelope glycoprotein sequences in eight African heterosexual transmission pairs and found that shorter V1, V2 and V4 length and fewer glycans are the common features shared by the sequences obtained from early transmitters (Derdeyn, C. A., et al. 2004. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303:2019-2022.). This data suggests that antigens that mimic such viruses might have relevance for the early-transmitted viruses. However, such early transmitter structures have not been observed for all subtypes (Chohan, B., et al. 2005. Selection for Human Immunodeficiency Virus Type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels. J. Virol. 79:6528-6531). However, incorporation of shorter V loops in an envelope immunogen may have other benefits, such as enhancement of sensitivity to soluble CD4 (Pickora, C., et al. 2005. Identification of two N-linked glycosylation sites within the core of the Simian Immunodificiency virus glycoprotein whose removal enhances sensitivity to soluble CD4. J. Virol. 79:12575-12583), and should be considered.
Studies have shown the importance of HIV-1 specific CTL responses in controlling viral load during acute and asymptomatic infection and the development of AIDS. However, it is unclear if current envelope based DNA vaccines are as potent as needed. Several methods have been used to increase the expression levels of HIV-1 immunogens, such as codon optimization (Andre, S., et al. 1998. Increased immune response elicited by DNA vaccination with a synthetic gp120 sequence with optimized codon usage. J Viral 72:1497-503; Deml, L., et al. A. 2001. Multiple effects of codon usage optimization on expression and immunogenicity of DNA candidate vaccines encoding the human immunodeficiency virus type 1 gag protein. J. Virol. 75:10991-11001), RNA optimization (Muthumani, K., et al. 2003. Novel engineered HIV-1 East African Clade-A gp160 plasmid construct induces strong humoral and cell-mediated immune responses in vivo. Virology 314:134-46; Schneider, R., M. et al. 1997. Inactivation of the human immunodeficiency virus type 1 inhibitory elements allows Rev-independent expression of Gag and Gag/protease and particle formation. J. Virol. 71:4892-4903) and the addition of immunoglobin leader sequences that have weak RNA secondary structure (Yang, J. S., et al. 2001. Induction of potent Th1-Type immune responses from a novel DNA vaccine for West Nile Virus New York Isolate (WNV-NY1999). J. Infect Diseases 184:809-816).
Human Papillomavirus (HPV) has a circular dsDNA genome (7,000-8,000 base pairs). There are up to 200 different genotypes. Phylogenetically, HPV is highly conserved. Mucosal HPV are Classified as “High Risk” or “Low Risk”. The Low Risk group includes types 6, 11, 42, and others. Associated Diseases include: Genital Warts; Low grade cervical, anal, vulvar, vaginal dysplasia; and Recurrent Respiratory Papillomatosis. The High Risk group includes types 16, 18, 31, 33, 45, 52, 58, and others. Associated Diseases include: Essential cause of Cervical cancer, pre-cancerous dysplasia; major cause of Anal, vulvar, vaginal, tonsillar cancer; and co-factor for other aerodigestive cancer. Every Day, 800 women die of cervical cancer.
HPV E6 and E7 proteins are tumor-specific antigens, required for tumorigenesis and maintenance of the tumor state. E7-specific immune responses are deleted in cervical cancer patients. Both E6 and E7 proteins interact specifically with the products of cellular human tumor suppressor genes, E6 with p53 and E7 with Rb (retinoblastoma tumor suppressor gene). E6 and E7 are ideal immunotherapeutic targets.
hTERT is a human telomerase reverse transcriptase that synthesizes a TTAGGG tag on the end of telomeres to prevent cell death due to chromosomal shortening. Embryonic cells and some germ line cells normally express hTERT to regulate homeostasis of cell populations. Cancer cells, however, exploit this mechanism of regulation to disrupt homeostasis of cell populations. For instance, hTERT over-expression occurs in more than 85% of human cancer cells. Therefore, hTERT is an ideal immunotherapeutic target.
hTERT may also enhance immunotherapeutics against hyperproliferating cells expressing hTERT due to HCV or HPV infection. The E6 oncoprotein from high-risk HPV types activates human telomerase reverse transcriptase (hTERT) transcription in human keratinocytes. Dysplastic legions and early neoplastic legions within the liver also express hTERT at abnormally high levels. Thus, immunotherapy against HPV and HCV may be enhanced by targeting cells that express hTERT at abnormal levels. Combination immunotherapy using both hTERT and HPV or HCV proteins or nucleic acids encoding such proteins is an attractive immunotherapy.
Influenza Hemagglutinin (HA) is expressed on the surface of Influenza viral particles and is responsible for initial contact between the virus and its host cell. HA is a well-known immunogen. Influenza A strain H1N5, an avian influenza strain, particularly threatens the human population because of its HA protein which, if slightly genetically reasserted by natural mutation, has greatly increased infectivity of human cells as compared to other strains of the virus. Infection of infants and older or immunocompromised adults humans with the viral H1N5 strain is often correlated to poor clinical outcome. Therefore, HA and other influenza molecules of the H1N5 strain of Influenza are ideal immunotherapeutic targets.